Macclesfield stretched their unbeaten run to four matches and inflicted Alfreton's fifth defeat in 10 games.
The hosts had started well, with Paul Clayton forcing Rhys Taylor into an early save, while Leigh Franks and Nathan Arnold having efforts blocked.
But Thierry Audel headed the Silkmen in front from John Paul Kissock's corner.
Clayton levelled with his 15th goal of the season from Josh Law's free-kick, but Waide Fairhurst headed the winner from Kieran Murtagh's cross.
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